Remember, your pen mill is basically four blades (plane/ chisel etc...) attached to one another. As such, many of the same principles apply, but with the addition of the four blades needing to be of equal. We also need to recognize the difference between sharpening and honing (cutlery folks are keen on this difference).
Sharpening is the cutting/ grinding of two intersecting surfaces to a point. Honing is orienting the point in a consistent manner. I learned quite a bit about this in watching one of Alton Brown's TV shows wherein he was discussing cutlery.
I must admit to having tried this method, but you can not sharpen a pen mill by rotating them against a flat surface. Think in terms of sharpening a plane blade by turning it perpindicular to the stone and rubbing the edge against the stone. When we do this with a pen mill, we are left rubbing a flat surface against the wood we are trying to cut. If it were done with an extremely light touch and on a very fine medium, it might cause a honing action (aligning the cutting edge). After thinking it through a bit, I will not use this method in the future.
As for grinding/ cutting the vertical surface of the mill, I think the primary value of this is honing (realigning the cutting edge). After continued use the cutting edge would likely be pushed down and this would push it back. However, one could eventually sharpen with this method, it would just take time. I think this is equivilant to sharpening a chisel or plane blade by continuously rubbing the back of the blade until it reaches the perfect intersect with the face of the blade. I will be giving this a go in terms of the honing benifit.
As for true sharpening, its just gotta be done like Paul in OKC, or the other guys were doing it with the small grinding wheels, backcutting the face of the blades. They are creating the true edge and are controlling the height of each blade.
I need to rig something like they did, cause I just keep buying new mills. Their method probably gets them sharper than when new!